Job ID = 14160350 SRX = SRX9567174 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24637979 spots for SRR13125149/SRR13125149.sra Written 24637979 spots for SRR13125149/SRR13125149.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160583 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:55:40 24637979 reads; of these: 24637979 (100.00%) were paired; of these: 9284342 (37.68%) aligned concordantly 0 times 12452525 (50.54%) aligned concordantly exactly 1 time 2901112 (11.77%) aligned concordantly >1 times ---- 9284342 pairs aligned concordantly 0 times; of these: 6433469 (69.29%) aligned discordantly 1 time ---- 2850873 pairs aligned 0 times concordantly or discordantly; of these: 5701746 mates make up the pairs; of these: 2763703 (48.47%) aligned 0 times 1355808 (23.78%) aligned exactly 1 time 1582235 (27.75%) aligned >1 times 94.39% overall alignment rate Time searching: 00:55:40 Overall time: 00:55:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 36 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 16685385 / 21775814 = 0.7662 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 09 Dec 2021 02:49:05: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:05: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:12: 1000000 INFO @ Thu, 09 Dec 2021 02:49:18: 2000000 INFO @ Thu, 09 Dec 2021 02:49:24: 3000000 INFO @ Thu, 09 Dec 2021 02:49:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:49:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 09 Dec 2021 02:49:35: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:35: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:37: 5000000 INFO @ Thu, 09 Dec 2021 02:49:44: 6000000 INFO @ Thu, 09 Dec 2021 02:49:44: 1000000 INFO @ Thu, 09 Dec 2021 02:49:50: 7000000 INFO @ Thu, 09 Dec 2021 02:49:52: 2000000 INFO @ Thu, 09 Dec 2021 02:49:57: 8000000 INFO @ Thu, 09 Dec 2021 02:50:01: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:50:04: 9000000 INFO @ Thu, 09 Dec 2021 02:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 09 Dec 2021 02:50:05: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:50:05: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:50:09: 4000000 INFO @ Thu, 09 Dec 2021 02:50:11: 10000000 INFO @ Thu, 09 Dec 2021 02:50:14: 1000000 INFO @ Thu, 09 Dec 2021 02:50:18: 5000000 INFO @ Thu, 09 Dec 2021 02:50:18: 11000000 INFO @ Thu, 09 Dec 2021 02:50:22: 2000000 INFO @ Thu, 09 Dec 2021 02:50:25: 12000000 INFO @ Thu, 09 Dec 2021 02:50:26: 6000000 INFO @ Thu, 09 Dec 2021 02:50:30: 3000000 INFO @ Thu, 09 Dec 2021 02:50:32: 13000000 INFO @ Thu, 09 Dec 2021 02:50:33: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:50:33: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:50:33: #1 total tags in treatment: 3670673 INFO @ Thu, 09 Dec 2021 02:50:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:50:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:50:33: #1 tags after filtering in treatment: 3107940 INFO @ Thu, 09 Dec 2021 02:50:33: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 09 Dec 2021 02:50:33: #1 finished! INFO @ Thu, 09 Dec 2021 02:50:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:50:33: #2 number of paired peaks: 912 WARNING @ Thu, 09 Dec 2021 02:50:33: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Thu, 09 Dec 2021 02:50:33: start model_add_line... INFO @ Thu, 09 Dec 2021 02:50:33: start X-correlation... INFO @ Thu, 09 Dec 2021 02:50:33: end of X-cor INFO @ Thu, 09 Dec 2021 02:50:33: #2 finished! INFO @ Thu, 09 Dec 2021 02:50:33: #2 predicted fragment length is 266 bps INFO @ Thu, 09 Dec 2021 02:50:33: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 09 Dec 2021 02:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05_model.r WARNING @ Thu, 09 Dec 2021 02:50:33: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:50:33: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 09 Dec 2021 02:50:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:50:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:50:35: 7000000 INFO @ Thu, 09 Dec 2021 02:50:39: 4000000 INFO @ Thu, 09 Dec 2021 02:50:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:43: 8000000 INFO @ Thu, 09 Dec 2021 02:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.05_summits.bed INFO @ Thu, 09 Dec 2021 02:50:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:50:48: 5000000 INFO @ Thu, 09 Dec 2021 02:50:52: 9000000 INFO @ Thu, 09 Dec 2021 02:50:56: 6000000 INFO @ Thu, 09 Dec 2021 02:51:00: 10000000 INFO @ Thu, 09 Dec 2021 02:51:05: 7000000 INFO @ Thu, 09 Dec 2021 02:51:09: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:51:14: 8000000 INFO @ Thu, 09 Dec 2021 02:51:17: 12000000 INFO @ Thu, 09 Dec 2021 02:51:23: 9000000 INFO @ Thu, 09 Dec 2021 02:51:26: 13000000 INFO @ Thu, 09 Dec 2021 02:51:27: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:27: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:27: #1 total tags in treatment: 3670673 INFO @ Thu, 09 Dec 2021 02:51:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:51:27: #1 tags after filtering in treatment: 3107940 INFO @ Thu, 09 Dec 2021 02:51:27: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 09 Dec 2021 02:51:27: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:27: #2 number of paired peaks: 912 WARNING @ Thu, 09 Dec 2021 02:51:27: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Thu, 09 Dec 2021 02:51:27: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:27: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:27: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:27: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:27: #2 predicted fragment length is 266 bps INFO @ Thu, 09 Dec 2021 02:51:27: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 09 Dec 2021 02:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10_model.r WARNING @ Thu, 09 Dec 2021 02:51:27: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:27: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 09 Dec 2021 02:51:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:51:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:51:31: 10000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:51:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:51:40: 11000000 INFO @ Thu, 09 Dec 2021 02:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:51:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.10_summits.bed INFO @ Thu, 09 Dec 2021 02:51:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (565 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:51:48: 12000000 INFO @ Thu, 09 Dec 2021 02:51:56: 13000000 INFO @ Thu, 09 Dec 2021 02:51:57: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:57: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:57: #1 total tags in treatment: 3670673 INFO @ Thu, 09 Dec 2021 02:51:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:51:57: #1 tags after filtering in treatment: 3107940 INFO @ Thu, 09 Dec 2021 02:51:57: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 09 Dec 2021 02:51:57: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:57: #2 number of paired peaks: 912 WARNING @ Thu, 09 Dec 2021 02:51:57: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Thu, 09 Dec 2021 02:51:57: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:57: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:57: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:57: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:57: #2 predicted fragment length is 266 bps INFO @ Thu, 09 Dec 2021 02:51:57: #2 alternative fragment length(s) may be 266 bps INFO @ Thu, 09 Dec 2021 02:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20_model.r WARNING @ Thu, 09 Dec 2021 02:51:57: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:57: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Thu, 09 Dec 2021 02:51:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:51:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:52:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567174/SRX9567174.20_summits.bed INFO @ Thu, 09 Dec 2021 02:52:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 1 millis CompletedMACS2peakCalling